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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| Package: DataQualityDashboard | ||
| Type: Package | ||
| Title: Execute and View Data Quality Checks on OMOP CDM Database | ||
| Version: 2.2.0 | ||
| Date: 2023-05-05 | ||
| Version: 2.3.0 | ||
| Date: 2023-05-21 | ||
| Authors@R: c( | ||
| person("Katy", "Sadowski", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Clair", "Blacketer", role = c("aut")), | ||
|
|
@@ -27,7 +27,7 @@ Imports: | |
| dplyr, | ||
| jsonlite, | ||
| rJava, | ||
| SqlRender (>= 1.6.0), | ||
| SqlRender (>= 1.10.1), | ||
| plyr, | ||
| stringr, | ||
| rlang, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| # Copyright 2023 Observational Health Data Sciences and Informatics | ||
| # | ||
| # This file is part of DataQualityDashboard | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
|
||
| #' @title Convert JSON results file case | ||
| #' | ||
| #' @description Convert a DQD JSON results file between camelcase and (all-caps) snakecase. Enables viewing of pre-v.2.1.0 results files in later DQD versions, and vice versa | ||
| #' | ||
| #' @param jsonFilePath Path to the JSON results file to be converted | ||
| #' @param writeToFile Whether or not to write the converted results back to a file (must be either TRUE or FALSE) | ||
| #' @param outputFolder The folder to output the converted JSON results file to | ||
| #' @param outputFile (OPTIONAL) File to write converted results JSON object to. Default is name of input file with a "_camel" or "_snake" postfix | ||
| #' @param targetCase Case into which the results file parameters should be converted (must be either "camel" or "snake") | ||
| #' | ||
| #' @returns DQD results object (a named list) | ||
| #' | ||
| #' @importFrom jsonlite fromJSON | ||
| #' @importFrom SqlRender snakeCaseToCamelCase camelCaseToSnakeCase | ||
| #' @importFrom dplyr rename_with | ||
| #' @importFrom tools file_path_sans_ext | ||
| #' | ||
| #' @export | ||
|
|
||
| convertJsonResultsFileCase <- function( | ||
| jsonFilePath, | ||
| writeToFile, | ||
| outputFolder = NA, | ||
| outputFile = "", | ||
| targetCase) { | ||
| if (!any(targetCase %in% c("camel", "snake"))) { | ||
| stop("targetCase must be either 'camel' or 'snake'.") | ||
| } | ||
| stopifnot(is.logical(writeToFile)) | ||
| if (writeToFile && is.na(outputFolder)) { | ||
| stop("You must specify an output folder if writing to file.") | ||
| } | ||
|
|
||
| results <- jsonlite::fromJSON(jsonFilePath) | ||
|
|
||
| if ("numViolatedRows" %in% names(results$CheckResults) && targetCase == "camel") { | ||
| warning("File is already in camelcase! No conversion will be performed.") | ||
| return(results) | ||
| } | ||
| if ("NUM_VIOLATED_ROWS" %in% names(results$CheckResults) && targetCase == "snake") { | ||
| warning("File is already in snakecase! No conversion will be performed.") | ||
| return(results) | ||
| } | ||
|
|
||
| if (targetCase == "camel") { | ||
| swapFunction <- SqlRender::snakeCaseToCamelCase | ||
| } else { | ||
| swapFunction <- function(x) { | ||
| toupper(SqlRender::camelCaseToSnakeCase(x)) | ||
| } | ||
| } | ||
|
|
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| results$Metadata <- dplyr::rename_with(results$Metadata, swapFunction) | ||
| results$CheckResults <- dplyr::rename_with(results$CheckResults, swapFunction, -c("checkId")) | ||
|
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||
| if (writeToFile) { | ||
| if (nchar(outputFile) == 0) { | ||
| jsonFile <- tools::file_path_sans_ext(basename(jsonFilePath)) | ||
| outputFile <- paste(jsonFile, "_", targetCase, ".json", sep = "") | ||
| } | ||
| .writeResultsToJson(results, outputFolder, outputFile) | ||
| } | ||
|
|
||
| return(results) | ||
| } |
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